Slit3 slit guidance ligand 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Slit3provided by RGD
Official Full Name: slit guidance ligand 3provided by RGD
Primary source: RGD:69311
See related: EnsemblRapid:ENSRNOG00000007377 AllianceGenome:RGD:69311
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Megf5
Summary: Predicted to enable Roundabout binding activity and heparin binding activity. Involved in spinal cord development. Predicted to be located in extracellular space. Biomarker of congenital diaphragmatic hernia. Orthologous to human SLIT3 (slit guidance ligand 3). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Lung (RPKM 171.9), Uterus (RPKM 79.2) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q12

Exon count:: 36

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (20075929..20660704)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (19571798..20156634)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (19924200..20517918)

Chromosome 10 - NC_086028.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Angelica sinensis polysaccharide improves rheumatoid arthritis by modifying the expression of intestinal Cldn5, Slit3 and Rgs18 through gut microbiota.
Title: Angelica sinensis polysaccharide improves rheumatoid arthritis by modifying the expression of intestinal Cldn5, Slit3 and Rgs18 through gut microbiota.
Relative mRNA expression of Ndst1 and Slit3 was significantly decreased in pleuroperitoneal folds, developing diaphragms and fully muscularized diaphragms, and endothelial cells within the diaphragmatic vasculature of nitrofen-exposed fetuses compared to controls.
Title: Down-regulation of N-deacetylase-N-sulfotransferase-1 signaling in the developing diaphragmatic vasculature of nitrofen-induced congenital diaphragmatic hernia.
The difference in expression pattern of Slit family mRNA in the neurons during peripheral nerve regeneration suggests that it plays a different role in axonal regeneration after axotomy of peripheral nerves
Title: mRNA expression changes of slit proteins following peripheral nerve injury in the rat model.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

BF405181 (e-PCR)
- UniSTS:247808

Slit3 (e-PCR), detects polymorphism
- UniSTS:463432

RH138151 (e-PCR)
- UniSTS:220238

BE108987 (e-PCR)
- UniSTS:247934

D10Rat113 (e-PCR)
- UniSTS:118150

RH143863 (e-PCR)
- UniSTS:233109

D10Rat45 (e-PCR)
- UniSTS:118186

D11Mit186 (e-PCR), detects polymorphism
- UniSTS:126382

BF399581 (e-PCR)
- UniSTS:247732

BG373360 (e-PCR)
- UniSTS:249270

AU048637 (e-PCR)
- UniSTS:145087

D10Mit16 (e-PCR), detects polymorphism
- UniSTS:226267

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables Roundabout binding	IBA Inferred from Biological aspect of Ancestor more info
enables Roundabout binding	IEA Inferred from Electronic Annotation more info
enables Roundabout binding	ISO Inferred from Sequence Orthology more info
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables heparin binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in Roundabout signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in Roundabout signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within animal organ morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in aortic valve morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in aortic valve morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in apoptotic process involved in luteolysis	IEA Inferred from Electronic Annotation more info
involved_in apoptotic process involved in luteolysis	ISO Inferred from Sequence Orthology more info
involved_in atrioventricular valve morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in atrioventricular valve morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in axon extension involved in axon guidance	IEA Inferred from Electronic Annotation more info
involved_in axon extension involved in axon guidance	ISO Inferred from Sequence Orthology more info
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within axon guidance	ISO Inferred from Sequence Orthology more info
involved_in axon guidance	ISO Inferred from Sequence Orthology more info
involved_in cellular response to hormone stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to hormone stimulus	ISO Inferred from Sequence Orthology more info
NOT involved_in chemorepulsion involved in embryonic olfactory bulb interneuron precursor migration	ISO Inferred from Sequence Orthology more info
involved_in negative chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in negative chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell growth	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cell growth	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell population proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of chemokine-mediated signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of chemokine-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in response to cortisol	IEA Inferred from Electronic Annotation more info
involved_in response to cortisol	ISO Inferred from Sequence Orthology more info
involved_in spinal cord development	IEP Inferred from Expression Pattern more info	PubMed
involved_in ventricular septum morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in ventricular septum morphogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in extracellular space	IEA Inferred from Electronic Annotation more info
located_in extracellular space	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: slit homolog 3 protein

Names: multiple EGF-like domains protein 5; multiple epidermal growth factor-like domains 5; multiple epidermal growth factor-like domains protein 5; slit-3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_031321.1 → NP_112611.1 slit homolog 3 protein precursor

See identical proteins and their annotated locations for NP_112611.1

Status: PROVISIONAL

Source sequence(s)

AB011531

UniProtKB/Swiss-Prot

O88280

UniProtKB/TrEMBL

F1LQL9

Related

ENSRNOP00000009714.7, ENSRNOT00000009714.7

Conserved Domains (12) summary

smart00013
Location:725 → 756

LRRNT; Leucine rich repeat N-terminal domain

smart00082
Location:857 → 906

LRRCT; Leucine rich repeat C-terminal domain

cd00054
Location:1074 → 1110

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

cd00116
Location:49 → 220

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

sd00033
Location:64 → 86

LRR_RI; leucine-rich repeat [structural motif]

pfam00008
Location:1123 → 1153

EGF; EGF-like domain

pfam01462
Location:33 → 60

LRRNT; Leucine rich repeat N-terminal domain

pfam02210
Location:1188 → 1314

Laminin_G_2; Laminin G domain

pfam12799
Location:331 → 371

LRR_4; Leucine Rich repeats (2 copies)

pfam13855
Location:775 → 835

LRR_8; Leucine rich repeat

cl15307
Location:437 → 467

TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

cl21545
Location:1463 → 1519

GHB_like; Glycoprotein hormone beta chain homologues